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comparison lordec_stat.xml @ 5:86ac3b90e9f6 draft

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author abretaud
date Wed, 31 Aug 2016 11:22:34 -0400
parents 46caddb8b8eb
children 529da747c89c
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4:f0b144292846 5:86ac3b90e9f6
1 <tool id="lordecstat" name="lordecstat" version="0.5.3"> 1 <tool id="lordecstat" name="lordecstat" version="0.5.3.1">
2 <description>is an efficient tool to generate statistics on solid and weak k-mers in PacBio corrected reads</description> 2 <description>is an efficient tool to generate statistics on solid and weak k-mers in PacBio corrected reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.3">lordec</requirement> 4 <requirement type="package" version="0.6">lordec</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command><![CDATA[
7 lordec-stat 7 lordec-stat
8 -2 $short_reads 8 -2 $short_reads
9 -i $long_reads 9 -i $long_reads
10 -k $kmer_len 10 -k $kmer_len
11 -s $solid_threshold 11 -s $solid_threshold
12 -S $stat_file 12 -S $stat_file
13 #if str( $advanced_options.advanced_options_selector) == "advanced" 13 #if str( $advanced_options.advanced_options_selector) == "advanced"
14 -T $advanced_options.threads 14 -T $advanced_options.threads
15 #end if 15 #end if
16 2&gt;1 16 2>&1
17 ]]>
17 </command> 18 </command>
18 19
19 <inputs> 20 <inputs>
20 <!-- Input data files --> 21 <!-- Input data files -->
21 <param name="short_reads" type="data" format="fasta,fastq.gz,fastq" label="short read FASTA/Q file" /> 22 <param name="short_reads" type="data" format="fasta,fastq.gz,fastq" label="short read FASTA/Q file" />
54 55
55 ------- 56 -------
56 57
57 **Integrated by** 58 **Integrated by**
58 59
59 Yvan Le Bras and Cyril Monjeaud 60 Yvan Le Bras and Cyril Monjeaud
60 61
61 GenOuest Bio-informatics Core Facility 62 GenOuest Bio-informatics Core Facility
62 63
63 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) 64 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
64 65
68 69
69 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_ 70 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
70 71
71 </help> 72 </help>
72 <citations> 73 <citations>
74 <citation type="doi">10.1186/s13742-015-0105-2</citation>
73 <citation type="doi">10.1093/bioinformatics/btu538</citation> 75 <citation type="doi">10.1093/bioinformatics/btu538</citation>
74 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013, 76 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
75 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, 77 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
76 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, 78 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
77 booktitle = {JOBIM 2013 Proceedings}, 79 booktitle = {JOBIM 2013 Proceedings},
78 year = {2013}, 80 year = {2013},
79 url = {https://www.e-biogenouest.org/resources/128}, 81 url = {https://www.e-biogenouest.org/resources/128},
80 pages = {97-106} 82 pages = {97-106}
81 }</citation> 83 }</citation>
82 </citations> 84 </citations>
83 </tool> 85 </tool>